11-62929479-A-G

Variant names:

• chr11-62929479-A-G
• rs1938677
• ENST00000782248.1:n.270-73A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000782248.1(ENSG00000301851):​n.270-73A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,944 control chromosomes in the GnomAD database, including 21,045 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (21045 hom., cov: 32)
• Consequence: ENSG00000301851 ENST00000782248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 4 publications found

Genes affected

ENSG00000301851 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782248.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301851	ENST00000782248.1		n.270-73A>G		intron	N/A
	ENSG00000301851	ENST00000782249.1		n.437-167A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79391 AN: 151826 Hom.: 21012 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.534

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.523 AC: 79471 AN: 151944 Hom.: 21045 Cov.: 32 AF XY: 0.530 AC XY: 39330 AN XY: 74242

African (AFR) AF: 0.457 AC: 18929 AN: 41418

American (AMR) AF: 0.619 AC: 9451 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1726 AN: 3468

East Asian (EAS) AF: 0.607 AC: 3132 AN: 5160

South Asian (SAS) AF: 0.632 AC: 3045 AN: 4816

European-Finnish (FIN) AF: 0.569 AC: 5996 AN: 10544

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35305 AN: 67958

Other (OTH) AF: 0.537 AC: 1129 AN: 2104

Alfa AF: 0.522 Hom.: 34682

Bravo AF: 0.524

Asia WGS AF: 0.625 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.73
PhyloP100		0.039

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1938677; hg19: chr11-62696951;